data_V3A
#
_chem_comp.id V3A
_chem_comp.name "9-{2-deoxy-5-O-[(R)-{[(R)-[(R)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-alpha-D-erythro-pentofuranosyl}-9H-purin-6-amine"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C11 H17 F N5 O11 P3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2018-03-22
_chem_comp.pdbx_modified_date 2018-06-29
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 507.199
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code V3A
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 6CR7
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
V3A PA P1 P 0 1 N N N 4.864 5.335 14.790 1.685 -1.585 -0.661 PA V3A 1
V3A O1A O1 O 0 1 N N N 3.789 5.474 15.820 1.441 -1.411 -2.243 O1A V3A 2
V3A O2A O2 O 0 1 N N N 6.172 5.580 15.440 2.269 -2.918 -0.395 O2A V3A 3
V3A O3A O3 O 0 1 N N N 4.935 3.884 14.203 2.696 -0.443 -0.146 O3A V3A 4
V3A "O5'" O4 O 0 1 N N N 4.606 6.363 13.545 0.281 -1.448 0.116 "O5'" V3A 5
V3A PB P2 P 0 1 N N N 3.771 2.796 13.912 4.285 -0.216 -0.274 PB V3A 6
V3A O2B O5 O 0 1 N N N 3.771 2.466 12.453 4.657 -0.125 -1.704 O2B V3A 7
V3A O1B O6 O 0 1 N N N 2.385 3.275 14.345 5.061 -1.454 0.404 O1B V3A 8
V3A C3B C1 C 0 1 N N R 4.264 1.303 14.826 4.748 1.329 0.574 C3B V3A 9
V3A F3B F1 F 0 1 N N N 3.871 0.208 14.147 4.075 2.405 -0.015 F3B V3A 10
V3A PG P3 P 0 1 N N N 3.615 1.246 16.530 6.548 1.587 0.429 PG V3A 11
V3A O1G O7 O 0 1 N N N 3.150 2.681 16.919 6.952 1.686 -1.126 O1G V3A 12
V3A O2G O8 O 0 1 N N N 4.729 0.805 17.469 6.957 2.952 1.178 O2G V3A 13
V3A O3G O9 O 0 1 N N N 2.483 0.320 16.599 7.260 0.449 1.052 O3G V3A 14
V3A "C5'" C2 C 0 1 N N N 3.308 6.646 13.076 -0.790 -2.381 -0.043 "C5'" V3A 15
V3A "C4'" C3 C 0 1 N N R 3.357 6.746 11.610 -1.969 -1.957 0.835 "C4'" V3A 16
V3A "O4'" O10 O 0 1 N N N 4.260 8.079 11.102 -2.514 -0.723 0.353 "O4'" V3A 17
V3A "C1'" C4 C 0 1 N N S 5.265 7.333 10.708 -3.876 -0.916 -0.060 "C1'" V3A 18
V3A N9 N1 N 0 1 Y N N 6.660 7.601 10.606 -4.681 0.263 0.270 N9 V3A 19
V3A C4 C5 C 0 1 Y N N 7.473 7.918 9.600 -5.853 0.641 -0.334 C4 V3A 20
V3A N3 N2 N 0 1 Y N N 7.354 8.256 8.274 -6.605 0.151 -1.314 N3 V3A 21
V3A C2 C6 C 0 1 Y N N 8.415 8.549 7.579 -7.713 0.761 -1.679 C2 V3A 22
V3A N1 N3 N 0 1 Y N N 9.683 8.554 8.081 -8.132 1.873 -1.105 N1 V3A 23
V3A C6 C7 C 0 1 Y N N 9.885 8.238 9.369 -7.447 2.437 -0.116 C6 V3A 24
V3A N6 N4 N 0 1 N N N 11.203 8.196 10.011 -7.895 3.603 0.481 N6 V3A 25
V3A C5 C8 C 0 1 Y N N 8.770 7.917 10.169 -6.257 1.823 0.310 C5 V3A 26
V3A N7 N5 N 0 1 Y N N 8.668 7.566 11.471 -5.327 2.100 1.256 N7 V3A 27
V3A C8 C9 C 0 1 Y N N 7.405 7.356 11.708 -4.404 1.183 1.237 C8 V3A 28
V3A "C2'" C10 C 0 1 N N N 4.673 6.241 9.765 -4.371 -2.148 0.739 "C2'" V3A 29
V3A "C3'" C11 C 0 1 N N S 3.972 5.656 11.066 -3.085 -3.021 0.763 "C3'" V3A 30
V3A "O3'" O11 O 0 1 N N N 3.128 4.471 10.789 -3.064 -3.863 1.917 "O3'" V3A 31
V3A H1 H1 H 0 1 N N N 4.180 5.688 16.659 1.059 -0.558 -2.491 H1 V3A 32
V3A H2 H2 H 0 1 N N N 1.799 3.267 13.597 4.864 -1.574 1.343 H2 V3A 33
V3A H3 H3 H 0 1 N N N 5.359 1.354 14.921 4.475 1.262 1.627 H3 V3A 34
V3A H4 H4 H 0 1 N N N 2.222 2.669 17.124 6.521 2.411 -1.599 H4 V3A 35
V3A H5 H5 H 0 1 N N N 4.469 0.010 17.918 7.902 3.152 1.141 H5 V3A 36
V3A H6 H6 H 0 1 N N N 2.958 7.598 13.502 -1.103 -2.400 -1.087 H6 V3A 37
V3A H7 H7 H 0 1 N N N 2.622 5.838 13.371 -0.454 -3.374 0.254 H7 V3A 38
V3A H8 H8 H 0 1 N N N 2.340 6.873 11.211 -1.638 -1.837 1.866 H8 V3A 39
V3A H9 H9 H 0 1 N N N 5.323 6.695 11.602 -3.922 -1.116 -1.131 H9 V3A 40
V3A H10 H10 H 0 1 N N N 8.283 8.805 6.538 -8.300 0.336 -2.480 H10 V3A 41
V3A H11 H11 H 0 1 N N N 11.907 8.437 9.343 -8.717 4.018 0.178 H11 V3A 42
V3A H12 H12 H 0 1 N N N 11.225 8.848 10.769 -7.386 4.005 1.202 H12 V3A 43
V3A H13 H13 H 0 1 N N N 7.006 7.030 12.657 -3.544 1.156 1.891 H13 V3A 44
V3A H14 H14 H 0 1 N N N 3.983 6.617 8.995 -4.672 -1.867 1.748 H14 V3A 45
V3A H15 H15 H 0 1 N N N 5.416 5.577 9.299 -5.181 -2.656 0.216 H15 V3A 46
V3A H16 H16 H 0 1 N N N 4.784 5.333 11.734 -2.999 -3.611 -0.150 H16 V3A 47
V3A H17 H17 H 0 1 N N N 3.364 3.768 11.383 -3.798 -4.490 1.960 H17 V3A 48
#
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
V3A C2 N1 DOUB Y N 1
V3A C2 N3 SING Y N 2
V3A N1 C6 SING Y N 3
V3A N3 C4 DOUB Y N 4
V3A C6 N6 SING N N 5
V3A C6 C5 DOUB Y N 6
V3A C4 C5 SING Y N 7
V3A C4 N9 SING Y N 8
V3A "C2'" "C1'" SING N N 9
V3A "C2'" "C3'" SING N N 10
V3A C5 N7 SING Y N 11
V3A N9 "C1'" SING N N 12
V3A N9 C8 SING Y N 13
V3A "C1'" "O4'" SING N N 14
V3A "O3'" "C3'" SING N N 15
V3A "C3'" "C4'" SING N N 16
V3A "O4'" "C4'" SING N N 17
V3A N7 C8 DOUB Y N 18
V3A "C4'" "C5'" SING N N 19
V3A O2B PB DOUB N N 20
V3A "C5'" "O5'" SING N N 21
V3A "O5'" PA SING N N 22
V3A PB O3A SING N N 23
V3A PB O1B SING N N 24
V3A PB C3B SING N N 25
V3A F3B C3B SING N N 26
V3A O3A PA SING N N 27
V3A PA O2A DOUB N N 28
V3A PA O1A SING N N 29
V3A C3B PG SING N N 30
V3A PG O3G DOUB N N 31
V3A PG O1G SING N N 32
V3A PG O2G SING N N 33
V3A O1A H1 SING N N 34
V3A O1B H2 SING N N 35
V3A C3B H3 SING N N 36
V3A O1G H4 SING N N 37
V3A O2G H5 SING N N 38
V3A "C5'" H6 SING N N 39
V3A "C5'" H7 SING N N 40
V3A "C4'" H8 SING N N 41
V3A "C1'" H9 SING N N 42
V3A C2 H10 SING N N 43
V3A N6 H11 SING N N 44
V3A N6 H12 SING N N 45
V3A C8 H13 SING N N 46
V3A "C2'" H14 SING N N 47
V3A "C2'" H15 SING N N 48
V3A "C3'" H16 SING N N 49
V3A "O3'" H17 SING N N 50
#
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
V3A SMILES ACDLabs 12.01 "P(=O)(O)(OP(O)(C(P(=O)(O)O)F)=O)OCC3OC(n1cnc2c1ncnc2N)CC3O"
V3A InChI InChI 1.03 "InChI=1S/C11H17FN5O11P3/c12-11(29(19,20)21)30(22,23)28-31(24,25)26-2-6-5(18)1-7(27-6)17-4-16-8-9(13)14-3-15-10(8)17/h3-7,11,18H,1-2H2,(H,22,23)(H,24,25)(H2,13,14,15)(H2,19,20,21)/t5-,6+,7-,11+/m0/s1"
V3A InChIKey InChI 1.03 AHVBRAYGASDMPK-QMWPFBOUSA-N
V3A SMILES_CANONICAL CACTVS 3.385 "Nc1ncnc2n(cnc12)[C@@H]3C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)[C@H](F)[P](O)(O)=O)O3"
V3A SMILES CACTVS 3.385 "Nc1ncnc2n(cnc12)[CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)[CH](F)[P](O)(O)=O)O3"
V3A SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "c1nc(c2c(n1)n(cn2)[C@@H]3C[C@@H]([C@H](O3)COP(=O)(O)OP(=O)([C@H](F)P(=O)(O)O)O)O)N"
V3A SMILES "OpenEye OEToolkits" 2.0.6 "c1nc(c2c(n1)n(cn2)C3CC(C(O3)COP(=O)(O)OP(=O)(C(F)P(=O)(O)O)O)O)N"
#
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
V3A "SYSTEMATIC NAME" ACDLabs 12.01 "9-{2-deoxy-5-O-[(R)-{[(R)-[(R)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-alpha-D-erythro-pentofuranosyl}-9H-purin-6-amine"
V3A "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "[(~{R})-[[[(2~{R},3~{S},5~{S})-5-(6-aminopurin-9-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]-fluoranyl-methyl]phosphonic acid"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
V3A "Create component" 2018-03-22 RCSB
V3A "Initial release" 2018-07-04 RCSB
#